X-103323975-T-G

Variant names:

• chrX-103323975-T-G
• rs5987515

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.67 (18708 hom., 21540 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 3 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.670 AC: 73960 AN: 110382 Hom.: 18704 Cov.: 22

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.645

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.670 AC: 74015 AN: 110439 Hom.: 18708 Cov.: 22 AF XY: 0.659 AC XY: 21540 AN XY: 32683

African (AFR) AF: 0.910 AC: 27678 AN: 30399

American (AMR) AF: 0.618 AC: 6442 AN: 10432

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 1751 AN: 2629

East Asian (EAS) AF: 0.591 AC: 2044 AN: 3461

South Asian (SAS) AF: 0.736 AC: 1863 AN: 2530

European-Finnish (FIN) AF: 0.467 AC: 2735 AN: 5855

Middle Eastern (MID) AF: 0.544 AC: 117 AN: 215

European-Non Finnish (NFE) AF: 0.572 AC: 30166 AN: 52733

Other (OTH) AF: 0.645 AC: 972 AN: 1508

Alfa AF: 0.478 Hom.: 2661

Bravo AF: 0.691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5987515; hg19: chrX-102578903;